calculateViterbi: Calculate the Viterbi sequence

Description Usage Arguments

Description

Calculate the Viterbi sequence

Usage

1
2
calculateViterbi(number_states, initial_prob, meiosis, number_snps, genotypes,
  pop_allele_freqs, positions_cM, error, gender_1, gender_2)

Arguments

number_states

Integer. The number of IBD states in the model

initial_prob

A numeric vector containing the initial state probabilities

meiosis

Integer. The number of meiosis separating the two isolates

number_snps

Integer. The number of SNPs

genotypes

A integer martix containing the genotype calls for a pair of isolates

pop_allele_freqs

A numeric vector of population allele frequencies

positions_cM

A numeric vector of SNP genetic map positions in cM

error

Numeric. The genotype error rate

gender_1

Integer. The MOI estimate of isolate 1

gender_2

Integer. The MOI estimate of isolate 2


bahlolab/isoRelate documentation built on May 11, 2019, 5:25 p.m.